Transmissible spongiform encephalopathies (TSEs or prion diseases) are a group of rare neurodegenerative diseases which include Creutzfeldt-Jakob disease (CJD) in humans, scrapie in sheep, bovine spongiform encephalopathy (BSE), and chronic wasting disease (CWD) in mule deer and elk. TSE infectivity can cross species barriers. The fact that BSE has infected humans in Great Britain and concerns that CWD may act similarly in the US underscores the importance of understanding TSE pathogenesis and developing effective therapeutics. The infectious agent of TSE diseases is called a prion and is largely composed of an abnormally refolded, protease resistant form (PrPSc) of the normal, protease-sensitive prion protein, PrPC. Susceptibility to infection can be influenced by amino acid homology between PrPC and PrPSc while differences in structure between PrPSc molecules are believed to encode strain phenotypes. My laboratory addresses many different aspects of prion diseases at both the molecular and pathogenic level. In particular, my studies focus on: 1) identifying the earliest events which occur during prion infection, 2) defining the molecular pathways involved in prion-associated neurodegeneration, 3) determining the molecular basis of prion strains, 4) determining how PrPC sequence and post-translational modifications influence PrPSc formation and disease phenotype and, 5) development of effective prion therapeutics. The precise function of PrPC remains elusive but may depend upon its cellular localization. In 2017, we published data showing that PrPC is present in brain mitochondria from 6 to 12 week old wild-type and transgenic mice in the absence of disease Faris et al. Sci. Rep. 7: 41556 (2017). Mitochondrial PrPC was fully processed and did not require a membrane anchor to localize to the mitochondria. We further showed that mitochondrial PrPC was present as a transmembrane isoform with the C-terminus facing the mitochondrial matrix and the N-terminus facing the intermembrane space. Our data show that PrPC can be found in mitochondria in the absence of disease, old age, mutation, or overexpression and suggest that PrPC may play a role in mitochondrial function. Although there is an increasing body of work suggesting that mitochondrial dysfunction is important in several neurodegenerative diseases, the role of mitochondria in prion pathogenesis is poorly understood. Our proteomic analysis of two different mouse prion models suggested that mitochondrial pathways of apoptosis were involved in the neurodegeneration associated with non-amyloid prion disease (J. Proteome Res. 13: 4620-4634 (2014), Annual Report 2014). In 2017, we published a paper demonstrating that there is significant mitochondrial dysfunction at the clinical stages of prion disease (Faris et al., J. Virol. (2017), e-pub ahead of print). A proteomic analysis of isolated brain mitochondria from clinically affected animals showed that several proteins involved in electron transport, mitochondrial dynamics, and mitochondrial protein synthesis were dysregulated. Our study is the first to look at mitochondrial function throughout the course of prion disease and has the potential to identify new targets for therapeutic intervention. Amino acid mismatches between PrPC and PrPSc influence the rate at which PrPSc forms and heterozygosity at key residues has the potential to significantly slow or even prevent disease transmission J Gen Virol 93: 2749-2756 (2012). In human PrPC, methionine/valine heterozygosity at codon 129 influences prion transmission and is a known resistance factor to sCJD ACTA Neuropathol 130: 159-170 (2015). It is possible that the ratio of PrPSc with methionine at codon 129 (PrPSc-M129) to PrPSc with valine at codon 129 (PrPSc-V129) determines the efficient transmission of prions in heterozygous cases of CJD. In 2017, we continued to monitor a long-term in vivo experiment to test the efficiency of transmission of codon 129 heterozygous cases of CJD. Transgenic mice overexpressing human PrPC with methionine at codon 129 were inoculated in 2016 with brain material from multiple heterozygous cases of CJD. We had previously determined the ratio of PrPSc-M129 to PrPSc-V129 in these cases (Moore et al. PLoS Pathog. 12: e1005416 (2016), Annual Report 2016). These experiments will determine the influence of the PrPSc allotype ratio on prion disease tempo and transmission and will provide important insights into the mechanisms underlying CJD progression in humans. In 2017, we continued in vivo work analyzing early events during prion infection following intracranial inoculation. These studies are designed to provide critical information about the events that occur during the first few hours following exposure to prions, including when formation of new PrPSc occurs and how PrPC is affected. A manuscript describing these results is in preparation. Finally, in 2017 we continued studies initiated in 2016 to determine how post-translational modifications may influence PrPSc formation and prion pathogenesis in different mouse models of prion infection. Using our new 6550 iFunnel QTOF single quadrupole LC mass spectrometer, we have analyzed post-translational protein modifications such as phosphorylation, acetylation, oxidation etc. in prion-infected versus uninfected mice. Some of these data were recently published in Faris et al., J. Virol. (2017). In addition, we are studying how cell-specific differences in PrPC glycosylation may influence PrPSc formation and prion infection of cells. Over the past year, we have developed new techniques to purify PrPC from cells and analyze its glycosylation state. These techniques are critical for successful completion of this project. Our studies will help to elucidate how post-translational modifications contribute not only to PrPSc formation but also to different prion disease phenotypes in vivo.